Team van Boxtel @ Princess Maxima Center

PTATO

PTa Analysis TOolkit

MutationalPatterns

R package for extracting and visualizing mutational patterns in base substitution catalogues

PrimerDesign

Tool to design primers on a vcf file (using primer3 software)

SMuRF

Somatic Mutations Rechecker and Filtering

NF-IAP

Illumina Analysis Pipeline in Nextflow

ELAN_tools

Utility scripts for elabjournal

GenotoxicEcoli

Genotoxin_assay

Data and code accompanying the research protocol: "Assessing the mutagenic impact of genotoxins in human umbilical cord-blood derived stem cells"

Identify_lowVAF_bulk_muts

Identify mutations that are clonally present in a clone but subclonally present in a bulk sample

MutSigPipe

Mutational signature selection and refitting pipeline

NF-SMuRF

Somatic Mutations Rechecker and Filtering

RNASeq-NF

RNASeq-NF is an NGS analysis pipeline for RNA expression quantification.

Target_capture_tools

Scripts to analyze targeted sequencing data

CallableLoci_processor

Combines CallableLoci bed files from control and experimental samples.

filterSomatic

Filter SNVs or Indels based on non genotype specific quality parameters.

IAP

Illumina analysis pipeline

INDELFI

Script for INDEL filtering

Mutation_accumulation_T21

Mutational_signature_refitting

Scripts to perform mutational signature refitting

MutationalPatterns_manuscript2_data_scripts

smMIPfil

script for smMIP data analysis

SNVFI

Single Nucleotide Variant Filtering

VAFchecker

Walker

Link germline mutations with somatic variants